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	Dataset summary
	Drug summary
	Umap of single cell types and conditions (resistant and sensitive)
	Comparison of cell composition between the resistant and sensitive groups
	Comparison of intra-tumor heterogeneity (ITH) and epithelial-mesenchymal transition (EMT) scores of malignant cells between the resistant and sensitive groups (This dataset does not contain this module)
	Difference of cell-cell interactions between the resistant and sensitive groups
	Differentially expressed genes (DEGs) between the resistant and sensitive groups for each cell type
	Mechanism analysis of drug resistance-related DEGs for each cell type in the pre-treatment samples
	Mechanism analysis of drug resistance-related DEGs for each cell type in the post-treatment samples
	Mechanism analysis of drug resistance-related DEGs for each cell type in one patient or cell lines (This dataset does not contain this module)
	MicroRNAs (miRNAs) regulating drug resistance-related DEGs for Malignant cells
	Motifs and transcription factors (TFs) regulating drug resistance-related DEGs for each cell type
•	Differentially expressed genes act as transcription factors

Dataset: GSE169246_PacTissue

Dataset summary for GSE169246_PacTissue

Datast information	Dataset	GSE169246_PacTissue
	PMID	34653365
	Raw data ID/link	NA
	Organism	Homo sapiens
	Source	patients
	Tissue	Tumor tissue
	Cancer type level1	Breast cancer
	Cancer type level2	Advanced triple-negative breast cancer (TNBC)
	Regimen	paclitaxel
	Drug type	Chemotherapy
	Sample size	pre (resistant 3, sensitive 3); post (resistant 4, sensitive 3)
	Cell number	67140
	Extract protocol	10x genomics
	Data processing	CellRanger 3.0.0
	Public date	Public on Sep 15, 2021
	Description	This dataset has 7 patients, 6 of whom have both pre -and post-treatment samples.

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Drug summary for GSE169246_PacTissue

Drug name	DrugBank ID	Drug type	Targets name	Targets uniprot ID
"Paclitaxel"	DB01229	small molecule	TUBB1; BCL2; MAP4; MAP2; MAPT; NR1I2	Q9H4B7; P10415; P27816; P11137; P10636; O75469

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Umap of single cell types and conditions (resistant and sensitive)

Umap of cell types and conditions (resistant and sensitive). If this dataset has both pre-treatment and post-treatment samples, the cell types were annotated together. If this dataset is a cell line dataset, the UMAP of cell clusters and the cell ratio of drug-resistant and sensitive groups within each cluster will also be shown. (If the image exists, the user can click on it to enlarge it in a new window.)

Umap of cell types

Umap of conditions

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Comparison of cell composition between the resistant and sensitive groups

In the pre-treatment samples, the cell composition of the resistant and sensitive groups were compared.
* represents significant difference. (If the image exists, the user can click on it to enlarge it in a new window.)

In the post-treatment samples, the cell composition of the resistant and sensitive groups were compared.
* represents significant difference. (If the image exists, the user can click on it to enlarge it in a new window.)

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Comparison of ITH and EMT scores of malignant cells between the resistant and sensitive groups

Comparison of ITH (intra-tumoral heterogeneity) and EMT (epithelial-mesenchymal transition) scores of malignant cells between the resistant and sensitive groups. ITH represents intratumoral heterogeneity, EMT represents epithelial mesenchymal transition, pre represents pre-treatment, post represents post-treatment, post2 represents longer post-treatment. (If the image exists, the user can click on it to enlarge it in a new window.)

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Difference of cell-cell interactions between the resistant and sensitive groups

In the pre-treatment samples, the difference in cell-cell interactions between the resistant and sensitive groups was compared. The numbers indicate the count of cell-cell interactions that were either higher or lower in the resistant group compared to the sensitive group. The dot plots of significant ligand-receptor pairs in the resistant group and sensitive group are subsequently displayed. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

resistant vs. sensitive

Dot plot of significant ligand-receptor pairs in the resistant group	Dot plot of significant ligand-receptor pairs in the sensitive group

In the post-treatment samples, the difference in cell-cell interactions between the resistant and sensitive groups was compared. The numbers indicate the count of cell-cell interactions that were either higher or lower in the resistant group compared to the sensitive group. The dot plots of significant ligand-receptor pairs in the resistant group and sensitive group are subsequently displayed. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

resistant vs. sensitive

Dot plot of significant ligand-receptor pairs in the resistant group	Dot plot of significant ligand-receptor pairs in the sensitive group

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. The difference in cell-cell interactions between the resistant and sensitive groups was compared. The numbers indicate the count of cell-cell interactions that were either higher or lower in the resistant group compared to the sensitive group. The dot plots of significant ligand-receptor pairs in the resistant group and sensitive group are subsequently displayed. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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Differentially expressed genes (DEGs) between the resistant and sensitive groups for each cell type

In the pre-treatment samples, the differentially expressed genes (|avg_log2FC|>0.25 & p_val_adj<0.05) between the resistant and sensitive groups for each cell type.

Gene symbol	Gene id	avg_log2FC	p_val	p_val_adj	pct.1	pct.2	Cell type	Timepoint
GZMB	ENSG00000100453	-1.02279	0.00e+00	0.00e+00	0.183	0.471	CD8+ T cells	pre
MX1	ENSG00000157601	-1.0812	0.00e+00	0.00e+00	0.157	0.561	CD8+ T cells	pre
IFITM1	ENSG00000185885	-1.21152	0.00e+00	0.00e+00	0.85	0.984	CD8+ T cells	pre
ISG15	ENSG00000187608	-1.25514	0.00e+00	0.00e+00	0.256	0.687	CD8+ T cells	pre
CXCL13	ENSG00000156234	-2.20225	0.00e+00	0.00e+00	0.08	0.532	CD8+ T cells	pre
HSPH1	ENSG00000120694	0.96838	0.00e+00	0.00e+00	0.706	0.624	CD4+ T cells	pre
KLF6	ENSG00000067082	0.961986	0.00e+00	0.00e+00	0.788	0.531	CD4+ T cells	pre
MALAT1	ENSG00000251562	0.864516	0.00e+00	0.00e+00	0.999	0.999	CD4+ T cells	pre
SLC2A3	ENSG00000059804	0.848327	0.00e+00	0.00e+00	0.631	0.45	CD4+ T cells	pre
TNFAIP3	ENSG00000118503	0.847942	0.00e+00	0.00e+00	0.832	0.709	CD4+ T cells	pre
HSPA1B	ENSG00000232804	0.763118	0.00e+00	0.00e+00	0.743	0.539	CD4+ T cells	pre
HSPD1	ENSG00000144381	0.755704	0.00e+00	0.00e+00	0.756	0.713	CD4+ T cells	pre
JUN	ENSG00000177606	0.715252	0.00e+00	0.00e+00	0.799	0.553	CD4+ T cells	pre
HSPA1A	ENSG00000237724	0.655471	0.00e+00	0.00e+00	0.786	0.627	CD4+ T cells	pre
PTPRC	ENSG00000262418	0.634952	0.00e+00	0.00e+00	0.859	0.811	CD4+ T cells	pre
RPS29	ENSG00000213741	0.626987	0.00e+00	0.00e+00	0.907	0.921	CD4+ T cells	pre
FOS	ENSG00000170345	0.617473	0.00e+00	0.00e+00	0.692	0.362	CD4+ T cells	pre
NEAT1	ENSG00000245532	0.60604	0.00e+00	1.35e-43	0.502	0.386	CD4+ T cells	pre
NR4A2	ENSG00000153234	0.578637	0.00e+00	0.00e+00	0.791	0.62	CD4+ T cells	pre
HSP90AB1	ENSG00000096384	0.57594	0.00e+00	0.00e+00	0.948	0.934	CD4+ T cells	pre
MYADM	ENSG00000179820	0.570714	0.00e+00	0.00e+00	0.495	0.316	CD4+ T cells	pre
AC016831.7	NA	0.564589	4.17e-31	8.53e-27	0.567	0.513	CD4+ T cells	pre
CD69	ENSG00000110848	0.528401	0.00e+00	0.00e+00	0.558	0.406	CD4+ T cells	pre
EZR	ENSG00000092820	0.520841	5.61e-45	1.21e-40	0.747	0.68	CD4+ T cells	pre
LMNA	ENSG00000160789	0.519746	0.00e+00	1.26e-44	0.514	0.373	CD4+ T cells	pre
RNF19A	ENSG00000034677	0.518463	0.00e+00	0.00e+00	0.417	0.253	CD4+ T cells	pre
IGKV3-20	ENSG00000282402	0.516149	0.00e+00	0.00e+00	0.413	0.257	CD4+ T cells	pre
TAGAP	ENSG00000164691	0.501747	0.00e+00	0.00e+00	0.585	0.44	CD4+ T cells	pre
CHORDC1	ENSG00000285023	0.479844	5.68e-39	1.16e-34	0.464	0.368	CD4+ T cells	pre
REL	ENSG00000162924	0.476995	3.95e-39	8.07e-35	0.559	0.459	CD4+ T cells	pre
CD44	ENSG00000026508	0.471187	0.00e+00	0.00e+00	0.671	0.582	CD4+ T cells	pre
HSP90AA1	ENSG00000080824	0.459783	9.19e-35	1.88e-30	0.968	0.978	CD4+ T cells	pre
RANBP2	ENSG00000153201	0.457412	5.30e-38	1.08e-33	0.4	0.287	CD4+ T cells	pre
CCNL1	ENSG00000163660	0.437202	0.00e+00	0.00e+00	0.513	0.378	CD4+ T cells	pre
ZFP36	ENSG00000128016	0.432729	1.40e-45	1.79e-41	0.865	0.766	CD4+ T cells	pre
MBNL1	ENSG00000152601	0.431129	1.19e-40	2.44e-36	0.559	0.472	CD4+ T cells	pre
FOSB	ENSG00000125740	0.427689	0.00e+00	0.00e+00	0.456	0.269	CD4+ T cells	pre
ITGB1	ENSG00000150093	0.42405	0.00e+00	0.00e+00	0.469	0.332	CD4+ T cells	pre
MT-ATP6	ENSG00000198899	0.423233	1.41e-35	2.89e-31	0.958	0.929	CD4+ T cells	pre
IGLV2-23	ENSG00000211660	0.422885	0.00e+00	0.00e+00	0.27	0.052	CD4+ T cells	pre
NFKB1	ENSG00000109320	0.414328	8.88e-35	1.82e-30	0.387	0.276	CD4+ T cells	pre
NR4A1	ENSG00000123358	0.414319	0.00e+00	0.00e+00	0.339	0.193	CD4+ T cells	pre
IL7R	ENSG00000168685	0.412061	1.82e-31	3.73e-27	0.709	0.641	CD4+ T cells	pre
EML4	ENSG00000143924	0.406936	1.14e-29	2.34e-25	0.559	0.493	CD4+ T cells	pre
ITK	ENSG00000113263	0.404653	1.72e-33	3.52e-29	0.394	0.297	CD4+ T cells	pre
STK4	ENSG00000101109	0.401987	0.00e+00	1.34e-41	0.629	0.536	CD4+ T cells	pre
NR4A3	ENSG00000119508	0.399511	2.42e-39	4.95e-35	0.323	0.203	CD4+ T cells	pre
RBM39	ENSG00000131051	0.391392	0.00e+00	2.20e-42	0.628	0.54	CD4+ T cells	pre
DUSP1	ENSG00000120129	0.387768	0.00e+00	0.00e+00	0.81	0.615	CD4+ T cells	pre
IGLV3-1	ENSG00000211673	0.386551	0.00e+00	0.00e+00	0.297	0.084	CD4+ T cells	pre

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In the post-treatment samples, the differentially expressed genes (|avg_log2FC|>0.25 & p_val_adj<0.05) between the resistant and sensitive groups for each cell type.

Gene symbol	Gene id	avg_log2FC	p_val	p_val_adj	pct.1	pct.2	Cell type	Timepoint
HSP90AA1	ENSG00000080824	0.996199	4.64e-21	9.49e-17	0.739	0.5	Plasma cells	post
HSPA1A	ENSG00000237724	0.985121	2.72e-13	5.57e-09	0.668	0.475	Plasma cells	post
HSPA1B	ENSG00000232804	0.942516	1.46e-14	2.98e-10	0.698	0.514	Plasma cells	post
HLA-A	ENSG00000227715	0.655509	1.09e-17	2.23e-13	0.563	0.277	Plasma cells	post
HSP90AB1	ENSG00000096384	0.533953	2.55e-12	5.22e-08	0.58	0.358	Plasma cells	post
IRF1	ENSG00000125347	0.523232	2.79e-13	5.70e-09	0.336	0.128	Plasma cells	post
HLA-C	ENSG00000206435	0.480022	2.49e-22	5.09e-18	0.984	0.904	Plasma cells	post
HLA-B	ENSG00000206450	0.469165	1.99e-22	4.07e-18	0.97	0.844	Plasma cells	post
PIM2	ENSG00000102096	0.450666	4.04e-12	8.26e-08	0.581	0.387	Plasma cells	post
HERPUD1	ENSG00000051108	0.440389	5.41e-07	1.11e-02	0.869	0.855	Plasma cells	post
UBC	ENSG00000150991	0.429236	1.85e-07	3.79e-03	0.846	0.77	Plasma cells	post
HSPD1	ENSG00000144381	0.416443	4.02e-10	8.22e-06	0.347	0.16	Plasma cells	post
UBB	ENSG00000170315	0.416273	7.86e-08	1.61e-03	0.596	0.429	Plasma cells	post
CD74	ENSG00000019582	0.415318	1.55e-11	3.17e-07	0.897	0.766	Plasma cells	post
HSPA8	ENSG00000109971	0.410156	8.19e-07	1.68e-02	0.562	0.379	Plasma cells	post
ISG20	ENSG00000172183	0.385565	4.93e-08	1.01e-03	0.556	0.418	Plasma cells	post
TMED9	ENSG00000184840	0.292476	7.35e-12	1.50e-07	0.455	0.238	Plasma cells	post
RPS6	ENSG00000137154	-0.255687	7.53e-11	1.54e-06	0.64	0.798	Plasma cells	post
RPL11	ENSG00000142676	-0.257969	8.25e-09	1.69e-04	0.685	0.823	Plasma cells	post
EEF1A1	ENSG00000156508	-0.260632	1.27e-08	2.60e-04	0.955	0.968	Plasma cells	post
RPS12	ENSG00000112306	-0.263238	1.13e-08	2.31e-04	0.737	0.84	Plasma cells	post
SLAMF7	ENSG00000026751	-0.264294	2.08e-14	4.24e-10	0.181	0.376	Plasma cells	post
RPL12	ENSG00000197958	-0.271902	1.41e-09	2.88e-05	0.562	0.745	Plasma cells	post
RPLP1	ENSG00000137818	-0.278809	2.15e-09	4.40e-05	0.991	0.972	Plasma cells	post
RPL36	ENSG00000130255	-0.279015	4.97e-11	1.02e-06	0.437	0.663	Plasma cells	post
RPL3	ENSG00000100316	-0.283099	3.96e-08	8.09e-04	0.804	0.879	Plasma cells	post
SELENOM	ENSG00000198832	-0.289504	4.50e-14	9.21e-10	0.283	0.5	Plasma cells	post
TIMP1	ENSG00000102265	-0.292763	5.16e-20	1.06e-15	0.116	0.319	Plasma cells	post
RPL6	ENSG00000089009	-0.294364	4.63e-08	9.48e-04	0.726	0.805	Plasma cells	post
RPL23A	ENSG00000198242	-0.294372	3.27e-08	6.69e-04	0.515	0.681	Plasma cells	post
RPS15A	ENSG00000134419	-0.300199	1.51e-09	3.09e-05	0.784	0.851	Plasma cells	post
TRAM1	ENSG00000067167	-0.3007	2.84e-18	5.80e-14	0.196	0.422	Plasma cells	post
RPS13	ENSG00000110700	-0.301786	2.55e-11	5.21e-07	0.602	0.784	Plasma cells	post
EEF2	ENSG00000167658	-0.302127	1.15e-11	2.34e-07	0.386	0.599	Plasma cells	post
EEF1D	ENSG00000273594	-0.304384	2.37e-09	4.86e-05	0.511	0.699	Plasma cells	post
RPL36A	ENSG00000241343	-0.30651	1.49e-23	3.04e-19	0.077	0.27	Plasma cells	post
PECAM1	ENSG00000261371	-0.306965	1.43e-17	2.92e-13	0.152	0.351	Plasma cells	post
RPL26	ENSG00000161970	-0.309933	1.16e-10	2.37e-06	0.622	0.784	Plasma cells	post
ZFP36	ENSG00000128016	-0.312773	3.36e-07	6.87e-03	0.291	0.436	Plasma cells	post
RPL30	ENSG00000156482	-0.315181	1.97e-12	4.02e-08	0.614	0.812	Plasma cells	post
RPS8	ENSG00000142937	-0.317671	7.39e-10	1.51e-05	0.881	0.894	Plasma cells	post
RPL17	ENSG00000265681	-0.319698	1.17e-11	2.39e-07	0.505	0.695	Plasma cells	post
RAB30	ENSG00000137502	-0.325649	9.72e-08	1.99e-03	0.189	0.316	Plasma cells	post
HSP90B1	ENSG00000166598	-0.328976	1.39e-10	2.84e-06	0.785	0.897	Plasma cells	post
KRTCAP2	ENSG00000163463	-0.330004	2.69e-17	5.49e-13	0.451	0.695	Plasma cells	post
MT-ND5	ENSG00000198786	-0.332837	1.55e-19	3.17e-15	0.646	0.883	Plasma cells	post
RPL37A	ENSG00000197756	-0.338855	2.32e-14	4.75e-10	0.408	0.663	Plasma cells	post
MGP	ENSG00000111341	-0.344788	3.35e-28	6.86e-24	0.078	0.294	Plasma cells	post
RPS4X	ENSG00000198034	-0.356383	2.30e-10	4.71e-06	0.904	0.915	Plasma cells	post
YPEL5	ENSG00000119801	-0.364389	8.97e-10	1.84e-05	0.203	0.355	Plasma cells	post

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This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. The following are differentially expressed genes (|avg_log2FC|>0.25 & p_val_adj<0.05) between the resistant and sensitive groups for each cell type.

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Mechanism analysis of drug resistance-related DEGs for each cell type in the pre-treatment samples

Enrichment results for 5 known drug-resistant mechanisms in malignant cells and 1 known mechanism in TME cells.The "Signature" column represents the differentially expressed genes (DEGs) used for enrichment. The "Geneset" column represents the genes included in this mechanism. The "Overlap" column represents the number of genes in the "Geneset" that are enriched in the "Signature". The "Enriched Genes" column represents the genes in the "Geneset" that are enriched in the "Signature". (If the image exists, the user can click on it to enlarge it in a new window.)

Enrichment results for 1 known drug resistance mechanisms in TME cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Regulation by the Disease Microenvironment	5.60e-03	5.60e-03	410	186	9	23467	B cells	BCL2,BRAF,NFKB1,TGFBR2,ZEB2,CXCR4,RHOB,VIM,MALAT1
Regulation by the Disease Microenvironment	1.20e-01	1.20e-01	240	186	4	23467	CD4+ T cells	NFKB1,HNRNPA2B1,LDHB,MALAT1
Regulation by the Disease Microenvironment	1.20e-01	1.20e-01	329	186	5	23467	CD8+ T cells	BRAF,NFKB1,HNRNPA2B1,MALAT1,TSPYL2
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	52	186	0	23467	cDCs	NA
Regulation by the Disease Microenvironment	5.90e-03	5.90e-03	270	186	7	23467	Mono_Macro	MMP9,CXCR4,IL1B,VIM,MALAT1,FBP1,TIMP2
Regulation by the Disease Microenvironment	2.80e-01	2.80e-01	41	186	1	23467	NK cells	TGFB1
Regulation by the Disease Microenvironment	1.00e+00	1.00e+00	9	186	0	23467	pDCs	NA
Regulation by the Disease Microenvironment	1.40e-01	1.40e-01	254	186	4	23467	Plasma cells	CXCR4,HNRNPA2B1,VIM,MALAT1

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group of pre-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Up-regulated Hallmark	Up-regulated KEGG	Up-regulated GO BP

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group of pre-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window.Complete files can be downloaded from the download section.)

Down-regulated Hallmark	Down-regulated KEGG	Down-regulated GO BP

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Mechanism analysis of drug resistance-related DEGs for each cell type in the post-treatment samples

Enrichment results for 5 known drug resistance mechanisms in malignant cells and 1 known mechanism in TME cells.The "Signature" column represents the differentially expressed genes (DEGs) used for enrichment. The "Geneset" column represents the genes included in this mechanism. The "Overlap" column represents the number of genes in the "Geneset" that are enriched in the "Signature". The "Enriched Genes" column represents the genes in the "Geneset" that are enriched in the "Signature". (If the image exists, the user can click on it to enlarge it in a new window.)

Enrichment results for 1 known drug resistance mechanisms in TME cells

Mechnism	Pval	FDR	Signature	Geneset	Overlap	Background	Cell type	Enriched Genes
Regulation by the Disease Microenvironment	7.70e-01	7.70e-01	186	186	1	23467	B cells	HNRNPA2B1
Regulation by the Disease Microenvironment	5.10e-02	5.10e-02	105	186	3	23467	CD4+ T cells	TGFB1,VIM,TSPYL2
Regulation by the Disease Microenvironment	2.60e-01	2.60e-01	124	186	2	23467	CD8+ T cells	CXCR4,TSPYL2
Regulation by the Disease Microenvironment	1.60e-01	1.60e-01	175	186	3	23467	cDCs	SNAI1,VIM,FBP1
Regulation by the Disease Microenvironment	1.00e-01	1.00e-01	224	186	4	23467	Mono_Macro	NFKB1,SNAI1,VIM,FBP1
Regulation by the Disease Microenvironment	3.60e-02	3.60e-02	228	186	5	23467	NK cells	CXCR4,HNRNPA2B1,STAT3,VIM,TSPYL2
Regulation by the Disease Microenvironment	1.50e-02	1.50e-02	24	186	2	23467	pDCs	VIM,MALAT1
Regulation by the Disease Microenvironment	4.60e-01	4.60e-01	77	186	1	23467	Plasma cells	VIM

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group of post-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Up-regulated Hallmark	Up-regulated KEGG	Up-regulated GO BP

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group of post-treatment samples. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Down-regulated Hallmark	Down-regulated KEGG	Down-regulated GO BP

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Mechanism analysis of drug resistance-related DEGs for each cell type in one patient or cell lines

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. Enrichment results for 5 known drug resistance mechanisms in malignant cells and 1 known mechanism in TME cells are shown here.The "Signature" column represents the differentially expressed genes (DEGs) used for enrichment. The "Geneset" column represents the genes included in this mechanism. The "Overlap" column represents the number of genes in the "Geneset" that are enriched in the "Signature". The "Enriched Genes" column represents the genes in the "Geneset" that are enriched in the "Signature". (If the image exists, the user can click on it to enlarge it in a new window.)

Hallmark, KEGG and GOBP enrichment results for up-regulated genes in resistant group. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

Hallmark, KEGG and GOBP enrichment results for down-regulated genes in resistant group. Only show the top 50 pathways with fdr<0.05. If certain cell types are not displayed, it means that there are no significant pathways based on DEGs in those cell types. (If the image exists, the user can click on it to enlarge it in a new window. Complete files can be downloaded from the download section.)

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MicroRNAs (miRNAs) regulating drug resistance-related DEGs for malignant cells

In the pre-treatment samples, the miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for malignant cells are shown here. If the gene does not have any miRNAs with a score greater than 80, it will not be shown. Here only the names of miRNAs with a score greater than 90 are shown, but some names will not be shown because of too many overlaps. (Complete files containing all datasets and cell types can be downloaded from the download section.)

Regulating up-regulated DEGs in resistant group	Regulating down-regulated DEGs in resistant group
This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.	This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.

In the post-treatment samples, the miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for Malignant cells are shown here. If the gene does not have any miRNAs with a score greater than 80, it will not be shown. Here only the names of miRNAs with a score greater than 90 are shown, but some names will not be shown because of too many overlaps. (Complete files containing all datasets and cell types can be downloaded from the download section.)

Regulating up-regulated DEGs in resistant group	Regulating down-regulated DEGs in resistant group
This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.	This dataset does not contain malignant cells, nor does it predict any miRNA that corresponds to the top10 DEGs.

This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. The miRNAs with a score greater than 80 that regulate the top10 abs(avg_log2FC) drug resistance-related DEGs for Malignant cells are shown here. Here only the names of miRNAs with a score greater than 80 are shown, but some names will not be shown because of too many overlaps. If the gene does not have any miRNAs with a score greater than 90, it will not be shown. (Complete files containing all datasets and cell types can be downloaded from the download section.)

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Motifs and transcription factors (TFs) regulating drug resistance-related DEGs for each cell type

In the pre-treatment samples, the motifs and TFs that regulate drug resistance-related DEGs for each cell type are shown here. (Complete files can be downloaded from the download section.)

Motifs and TFs regulating up-regulated DEGs in resistant group of the pre-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	cisbp__M00775	3.6	0.124	ZBTB1 (inferredBy_Orthology).	B cells
	transfac_pro__M00514	3.53	0.122	ATF4 (directAnnotation).	B cells
	metacluster_126.2	3.48	0.121	ZBTB4; ZBTB4 (directAnnotation).	B cells
	metacluster_67.2	3.44	0.12	ZNF501 (directAnnotation). ACAA1; E2F2; E2F2; E2F3; E2F3; FOXN4 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__ETV5_HES7_CCGGAANNNNNNCACGTG_CAP	3.36	0.118	ETV5; HES7 (directAnnotation).	B cells
	taipale_cyt_meth__ZNF460_NRMCGCCCCCCGN_eDBD_meth	3.36	0.118	ZNF460 (directAnnotation).	B cells
	metacluster_3.10	3.32	0.117	KLF2; KLF4 (directAnnotation).	B cells
	transfac_pro__M07436	3.31	0.117	WT1 (directAnnotation).	B cells
	cisbp__M00249	3.3	0.117	WT1 (directAnnotation).	B cells
	taipale_cyt_meth__E2F2_NCGCGCGCGCM_eDBD_meth	3.3	0.117	E2F2 (directAnnotation).	B cells

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Motifs and TFs regulating down-regulated DEGs in resistant group of the pre-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	hdpi__FLI1	7.1	0.0886	FLI1 (directAnnotation).	B cells
	metacluster_2.8	5.67	0.0748	IRF4; IRF5; IRF6; IRF9 (directAnnotation). IRF3; IRF5; IRF5; IRF6 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__ETS2_RCCGGAAGTG_HT	5.56	0.0737	ETS2 (directAnnotation).	B cells
	taipale_tf_pairs__TEAD4_ETV1_RSCGGAAATRCM_CAP	4.67	0.0652	ETV1; TEAD4 (directAnnotation).	B cells
	tfdimers__MD00007	4.66	0.065	E2F1; IRF8 (directAnnotation).	B cells
	taipale_tf_pairs__ELF2_NATGCGGAAGTR_HT	4.57	0.0642	ELF2 (directAnnotation).	B cells
	taipale_tf_pairs__GCM1_ETV4_RTGCGGGCGGAAGTR_CAP	4.48	0.0634	ETV4; GCM1 (directAnnotation).	B cells
	jaspar__MA1708.1	4.4	0.0626	ETV7 (directAnnotation).	B cells
	transfac_pro__M06839	4.32	0.0618	ZNF263 (inferredBy_Orthology).	B cells
	taipale_tf_pairs__ELK1_HOXA1_RCCGGAAGTAATTA_HT	4.17	0.0604	ELK1; HOXA1 (directAnnotation).	B cells

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In the post-treatment samples, the motifs and TFs that regulate drug resistance-related DEGs for each cell type are shown here. (Complete files can be downloaded from the download section.)

Motifs and TFs regulating up-regulated DEGs in resistant group of the post-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	hocomoco__TYY2_HUMAN.H11MO.0.D	6.62	0.104	YY2 (directAnnotation).	B cells
	metacluster_141.2	6.22	0.0989	E2F2; E2F3 (directAnnotation).	B cells
	metacluster_21.4	5.73	0.0929	HSF1; HSF1; HSF2 (directAnnotation). HSF1; HSF2; HSF4; HSF5; HSFX1; HSFX2; HSFX3; HSFX4; HSFY1; HSFY2 (inferredBy_Orthology).	B cells
	metacluster_21.5	5.36	0.0882	HOXB2; HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF2; HSF2; HSF2; HSF2; HSF2; HSF2; HSF4; HSF4; HSF4 (directAnnotation). HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF1; HSF2; HSF2; HSF2; HSF2; HSF4; HSF4; HSF4; HSF4; HSF5; HSF5; HSF5; HSF5; HSFX1; HSFX1; HSFX1; HSFX1; HSFX2; HSFX2; HSFX2; HSFX2; HSFX3; HSFX3; HSFX3; HSFX3; HSFX4; HSFX4; HSFX4; HSFX4; HSFY1; HSFY1; HSFY1; HSFY1; HSFY2; HSFY2; HSFY2; HSFY2 (inferredBy_Orthology).	B cells
	metacluster_56.5	5.34	0.088	HSF1; HSF1; HSF2 (directAnnotation). HSF1; HSF2; HSF4; HSF5; HSFX1; HSFX2; HSFX3; HSFX4; HSFY1; HSFY2 (inferredBy_Orthology).	B cells
	flyfactorsurvey__pho_SOLEXA_F1-3	4.91	0.0826	YY1 (inferredBy_Orthology).	B cells
	metacluster_174.3	4.86	0.082	MBD2; NFYA; NFYB; NFYC; PBX3 (directAnnotation).	B cells
	swissregulon__hs__HSF2	4.86	0.082	HSF2 (directAnnotation).	B cells
	taipale__YY2_DBD_NNCCGCCATNW_repr	4.67	0.0797	YY2 (directAnnotation).	B cells
	metacluster_174.2	4.54	0.0781	CEBPZ; CEBPZ; DRAP1; FOS; FOXI1; FOXI1; HMGXB3; IRF3; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYA; NFYB; NFYB; NFYB; NFYB; NFYB; NFYC; NFYC; NFYC; NFYC; NFYC; NFYC; NFYC; PBX3; PBX3; SP2 (directAnnotation). NFYA; NFYA; NFYC; PBX1; PBX3 (inferredBy_Orthology).	B cells

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Motifs and TFs regulating down-regulated DEGs in resistant group of the post-treatment samples

motif	motif	NES	AUC	TF_highConf	Cell_type
	metacluster_155.13	5.13	0.109	ZNF135 (directAnnotation).	B cells
	metacluster_140.1	4.69	0.102	BCL11B; BCL11B (directAnnotation).	B cells
	taipale_tf_pairs__TEAD4_SPDEF_RGAATGCGGATN_CAP	4.35	0.0961	SPDEF; TEAD4 (directAnnotation).	B cells
	taipale_tf_pairs__ETV2_SOX15_RSCGGAWNNNNNNNACAATRN_CAP_repr	4.3	0.0951	ETV2; SOX15 (directAnnotation).	B cells
	transfac_pro__M06433	4.29	0.0951	ZNF571 (directAnnotation).	B cells
	transfac_pro__M05545	4.25	0.0944	IKZF4 (inferredBy_Orthology).	B cells
	tfdimers__MD00542	3.98	0.0899	E2F1; EBF1 (directAnnotation).	B cells
	tfdimers__MD00016	3.92	0.0888	MYCN (directAnnotation).	B cells
	taipale_tf_pairs__HOXB2_HOXB13_NNATCATNGTAAA_CAP_repr	3.87	0.088	HOXB13; HOXB2 (directAnnotation).	B cells
	transfac_pro__M06073	3.84	0.0875	ZNF749 (directAnnotation).	B cells

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This dataset only has one patient or is a cell line dataset, the resistant sample is the post-treatment sample and the sensitive sample is the pre-treatment sample. Motifs and TFs that regulate drug resistance-related DEGs for each cell type are shown here. (Complete files can be downloaded from the download section.)

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Differentially expressed genes act as transcription factors

This table shows the differentially expressed genes that act as transcription factors. (Complete files can be downloaded from the download section.)

TF	motif	Expression	Cell type	Timepoint
BATF	metacluster_50.1	up	CD4+ T cells	post
JUN	metacluster_50.1	up	CD4+ T cells	post
JUNB	metacluster_50.1	up	CD4+ T cells	post
BATF	metacluster_157.2	up	CD4+ T cells	post
JUN	metacluster_157.2	up	CD4+ T cells	post
JUNB	metacluster_157.2	up	CD4+ T cells	post
JUN	tfdimers__MD00165	up	CD4+ T cells	post
JUNB	tfdimers__MD00165	up	CD4+ T cells	post
JUN	cisbp__M01816	up	CD4+ T cells	post
IRF7	metacluster_2.6	up	CD8+ T cells	post

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1	"Sun X, Zhang Y, Li H, Zhou Y, Shi S, Chen Z, He X, Zhang H, Li F, Yin J, Mou M, Wang Y, Qiu Y, Zhu F. DRESIS: the first comprehensive landscape of drug resistance information. Nucleic Acids Res. 2023 Jan 6;51(D1):D1263-D1275. doi: 10.1093/nar/gkac812. PMID: 36243960; PMCID: PMC9825618."
2	"Wishart DS, Feunang YD, Guo AC, Lo EJ, Marcu A, Grant JR, Sajed T, Johnson D, Li C, Sayeeda Z, Assempour N, Iynkkaran I, Liu Y, Maciejewski A, Gale N, Wilson A, Chin L, Cummings R, Le D, Pon A, Knox C, Wilson M. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res. 2018 Jan 4;46(D1):D1074-D1082. doi: 10.1093/nar/gkx1037. PMID: 29126136; PMCID: PMC5753335."